snATACseq analysis with ArchR.

Results

QC

ArchR pre-filters the cells using 2 metrics:

  • TSS Enrichment > 4
  • Min frags per cell > 3000

Counts

Sample Cells_Pass_Filter Cells_dropped Total_Frags Median_Frags Median_TSS_Enrichment
510_FC 7011 219 141701588 15242 14.259
611_FC 3869 161 89911016 16830 11.868
993_FC 5273 207 62967252 5871 9.037

Doublet removal

Post-doublet removal numbers are the final cell numbers moving forward.

Sample Pre_DoubRem Post_DoubRem pc_cells_removed
510_FC_ATAC 7011 6520 7.003281
611_FC_ATAC 3869 3720 3.851124
993_FC_ATAC 5273 4995 5.272141

Pre-filter plots

TSS enrichment vs. log10(Number of fragments) - these are the pre-filtered results

If you want to compare these results to others studies check out page 4 of the ArchR supplementary document.

Post-filter plots

TSS enrichment vs. log10(Number of fragments) plot - all samples combined

Fragment size plot

TSS plot

Ridge plot

Cluster plots

UMAPs

Unconstrained Integration

Cluster mappings

RNA ExN-4 RG-1 ExN-2 N-undef InN-1 RG-1 ExN-3 InN-3 RG-1 ExN-2 MG InN-2 ExN-5 RG-2 InN-2 ExN-2
ATAC C1 C15 C8 C10 C4 C11 C12 C9 C16 C7 C13 C5 C2 C14 C6 C3

Cell counts

UMAP